[gmx-users] g_hbond tool question

[Carlos Navarro Retamal]

Dear gromacs users,  
I’m studying the hydrogen bond interaction between a protein and different solvents.To do that i’m using the g_hbond tools of gromacs (4.6.3 version).
As groups,I started using ‘Protein’ and ‘Sol’ and i got an specific number.
After that, to analyse the interaction in a more specific way between this 2 groups, i ran the g_hbond tools using different groups:
'MainChain+Cb' - 'SOL'
'MainChain+H'   - ‘SOL'
'SideChain'        -  'SOL'
'SideChain+H’   -  ‘SOL’
But when i sum hbond got by these four selections i got different values (higher) than the values got from ‘Protein’ - ‘SOL’
Why is this happening? Am i interpreting in a wrong way what the selection ‘Protein’ - ‘SOL’ is considering?
Hope someone can help me.
Thanks in advances,
Carlos


--  
Carlos Navarro Retamal
Bioinformatic engineer
Ph.D(c) in Applied Science, Universidad de Talca, Chile
Center of Bioinformatics and Molecular Simulations (CBSM)
Universidad de Talca
2 Norte 685, Casilla 721, Talca - Chile   
Teléfono: 56-71-201 798,  
Fax: 56-71-201 561
Email: carlos.navarro87 at gmail.com or cnavarro at utalca.cl